The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>

Inheritance diagram for MRMTransitionGroupPicker:

Public Member Functions
template<typename SpectrumT , typename TransitionT >
void	pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)
	Pick a group of chromatograms belonging to the same peptide. More...

template<typename SpectrumT , typename TransitionT >
MRMFeature	createMRMFeature (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, const int chr_idx, const int peak_idx)
	Create feature from a vector of chromatograms and a specified peak. More...

template<typename SpectrumT >
void	remove_overlapping_features (std::vector< SpectrumT > &picked_chroms, double best_left, double best_right)
	Remove overlapping features. More...

void	findLargestPeak (std::vector< MSChromatogram > &picked_chroms, int &chr_idx, int &peak_idx)
	Find largest peak in a vector of chromatograms. More...


	MRMTransitionGroupPicker ()
	Constructor. More...

	~MRMTransitionGroupPicker ()
	Destructor. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	updateMembers_ ()
	Synchronize members with param class. More...

MRMTransitionGroupPicker &	operator= (const MRMTransitionGroupPicker &rhs)
	Assignment operator is protected for algorithm. More...

template<typename SpectrumT , typename TransitionT >
const SpectrumT &	selectChromHelper_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, String native_id)
	Select matching precursor or fragment ion chromatogram. More...

template<typename SpectrumT , typename TransitionT >
double	computeQuality_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, const int chr_idx, const double best_left, const double best_right, String &outlier)
	Compute transition group quality (higher score is better) More...

template<typename SpectrumT >
void	recalculatePeakBorders_ (std::vector< SpectrumT > &picked_chroms, double &best_left, double &best_right, double max_z)
	Recalculate the borders of the peak. More...

void	calculateBgEstimation_ (const MSChromatogram &chromatogram, double best_left, double best_right, double &background, double &avg_noise_level)
	Will use the chromatogram to estimate the background noise and then subtract it. More...

Resampling methods
template<typename SpectrumT >
void	prepareMasterContainer_ (const SpectrumT &ref_chromatogram, SpectrumT &master_peak_container, double left_boundary, double right_boundary)
	Create an empty master peak container that has the correct mz / RT values set. More...

template<typename SpectrumT >
SpectrumT	resampleChromatogram_ (const SpectrumT &chromatogram, const SpectrumT &master_peak_container, double left_boundary, double right_boundary)
	Resample a container at the positions indicated by the master peak container. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
String	background_subtraction_

bool	recalculate_peaks_

bool	use_precursors_

bool	compute_peak_quality_

double	min_qual_

int	stop_after_feature_

double	stop_after_intensity_ratio_

double	min_peak_width_

double	recalculate_peaks_max_z_

double	resample_boundary_

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
stop_after_feature	int	-1		Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio	float	0.0001		Stop after reaching intensity ratio
min_peak_width	float	-1		Minimal peak width (s), discard all peaks below this value (-1 means no action).
background_subtraction	string	none	none, smoothed, original	Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.
recalculate_peaks	string	false	true, false	Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large.
use_precursors	string	false	true, false	Use precursor chromatogram for peak picking
recalculate_peaks_max_z	float	1		Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).
minimal_quality	float	-10000		Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary	float	15		For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_quality	string	false	true, false	Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.
PeakPickerMRM:sgolay_frame_length	int	15		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
PeakPickerMRM:sgolay_polynomial_order	int	3		Order of the polynomial that is fitted.
PeakPickerMRM:gauss_width	float	50		Gaussian width in seconds, estimated peak size.
PeakPickerMRM:use_gauss	string	true	false, true	Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
PeakPickerMRM:peak_width	float	-1		Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
PeakPickerMRM:signal_to_noise	float	1	min: 0	Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
PeakPickerMRM:sn_win_len	float	1000		Signal to noise window length.
PeakPickerMRM:sn_bin_count	int	30		Signal to noise bin count.
PeakPickerMRM:write_sn_log_messages	string	true	true, false	Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
PeakPickerMRM:remove_overlapping_peaks	string	false	false, true	Try to remove overlapping peaks during peak picking
PeakPickerMRM:method	string	corrected	legacy, corrected, crawdad	Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

It is called through pickTransitionGroup which will accept an MRMTransitionGroup filled with n chromatograms and perform the following steps:

Step 1: find features (peaks) in individual chromatograms
Step 2: merge these features to consensus features that span multiple chromatograms

Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.

Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.

Constructor & Destructor Documentation

◆ MRMTransitionGroupPicker()

MRMTransitionGroupPicker ( )

Constructor.

◆ ~MRMTransitionGroupPicker()

~MRMTransitionGroupPicker ( )

Destructor.

Member Function Documentation

◆ calculateBgEstimation_()

void calculateBgEstimation_	(	const MSChromatogram &	chromatogram,
		double	best_left,
		double	best_right,
		double &	background,
		double &	avg_noise_level
	)

protected

Will use the chromatogram to estimate the background noise and then subtract it.

The background is estimated by averaging the noise on either side of the peak and then subtracting that from the total intensity.

◆ computeQuality_()

double computeQuality_	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		std::vector< SpectrumT > &	picked_chroms,
		const int	chr_idx,
		const double	best_left,
		const double	best_right,
		String &	outlier
	)

inlineprotected

Compute transition group quality (higher score is better)

This is only based on the co-elution of the chromatograms and internal consistency without any library information.

For the final score (larger is better), consider these scores:

missing_peaks (the more peaks are missing, the worse)
multiple_peaks
mean of the shapes (1 is very good, 0 is bad)
mean of the coelutions (0 is good, 1 is ok, above 1 is pretty bad)

These scores are similar to the ones computed by MRMFeatureFinderScoring and a simple sum of these scores is returned.

left_borders / right_borders might not have the same length since we might have peaks missing!!

References OpenMS::Constants::k, LOG_DEBUG, mean_and_stddev::mean(), OpenSwath::Scoring::normalizedCrossCorrelation(), and OpenSwath::Scoring::xcorrArrayGetMaxPeak().

◆ createMRMFeature()

MRMFeature createMRMFeature	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		std::vector< SpectrumT > &	picked_chroms,
		const int	chr_idx,
		const int	peak_idx
	)

inline

Create feature from a vector of chromatograms and a specified peak.

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), Feature::getConvexHulls(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatograms(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitionGroupID(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitions(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), OpenMS::Constants::k, LOG_DEBUG, LOG_WARN, OPENMS_PRECONDITION, ConvexHull2D::setHullPoints(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), Peak2D::setMZ(), Feature::setOverallQuality(), Feature::setQuality(), and Peak2D::setRT().

◆ findLargestPeak()

void findLargestPeak	(	std::vector< MSChromatogram > &	picked_chroms,
		int &	chr_idx,
		int &	peak_idx
	)

Find largest peak in a vector of chromatograms.

◆ operator=()

MRMTransitionGroupPicker& operator= ( const MRMTransitionGroupPicker & rhs )

protected

Assignment operator is protected for algorithm.

◆ pickTransitionGroup()

void pickTransitionGroup ( MRMTransitionGroup< SpectrumT, TransitionT > & transition_group )

inline

Pick a group of chromatograms belonging to the same peptide.

Will identify peaks in a set of chromatograms that belong to the same peptide. The chromatograms are given in the MRMTransitionGroup container which also contains the mapping of the chromatograms to their metadata. Only chromatograms from detecting transitions are used for peak picking. Identifying transitions will be processed alongside but do not contribute to the meta-data, e.g. total_xic or peak_apices_sum.

The resulting features are added to the MRMTransitionGroup. Each feature contains the following meta-data:

PeptideRef
leftWidth
rightWidth
total_xic (fragment trace XIC sum)
peak_apices_sum

◆ prepareMasterContainer_()

void prepareMasterContainer_	(	const SpectrumT &	ref_chromatogram,
		SpectrumT &	master_peak_container,
		double	left_boundary,
		double	right_boundary
	)

inlineprotected

Create an empty master peak container that has the correct mz / RT values set.

The empty master peak container fill be filled with mz / RT values at the positions where the reference chromatogram has values. The container will only be populated between the boundaries given. The output container will contain peaks with mz / RT values but all intensity values will be zero.

Parameters

ref_chromatogram	Reference chromatogram containing mz / RT values (possibly beyond the desired range)
master_peak_container	Output container to be populated
left_boundary	Left boundary of values the container should be populated with
right_boundary	Right boundary of values the container should be populated with

References OPENMS_PRECONDITION.

◆ recalculatePeakBorders_()

void recalculatePeakBorders_	(	std::vector< SpectrumT > &	picked_chroms,
		double &	best_left,
		double &	best_right,
		double	max_z
	)

inlineprotected

Recalculate the borders of the peak.

By collecting all left and right borders of contained peaks, a consensus peak is computed. By looking at the means and standard deviations of all the peak borders it is estimated whether the proposed peak border deviates too much from the consensus one. If the deviation is too high (in this case), then we fall back to the "consensus" (a median here).

References OpenMS::Constants::k, LOG_DEBUG, and OpenMS::Math::mean().

◆ remove_overlapping_features()

void remove_overlapping_features	(	std::vector< SpectrumT > &	picked_chroms,
		double	best_left,
		double	best_right
	)

inline

Remove overlapping features.

Remove features that are within the current seed (between best_left and best_right) or overlap with it. An overlapping feature is defined as a feature that has either of its borders within the border of the current peak

Directly adjacent features are allowed, e.g. they can share one border.

References OpenMS::Constants::k.

◆ resampleChromatogram_()

SpectrumT resampleChromatogram_	(	const SpectrumT &	chromatogram,
		const SpectrumT &	master_peak_container,
		double	left_boundary,
		double	right_boundary
	)

inlineprotected

Resample a container at the positions indicated by the master peak container.

Parameters

chromatogram	Container with the input data
master_peak_container	Container with the mz / RT values at which to resample
left_boundary	Left boundary of values the container should be resampled
right_boundary	Right boundary of values the container should be resampled

Returns: A container which contains the data from the input chromatogram resampled at the positions of the master container

References LinearResamplerAlign::raster().

◆ selectChromHelper_()

const SpectrumT& selectChromHelper_	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		String	native_id
	)

inlineprotected

Select matching precursor or fragment ion chromatogram.

References MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), and MRMTransitionGroup< ChromatogramType, TransitionType >::hasPrecursorChromatogram().

◆ updateMembers_()

void updateMembers_ ( )

protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ background_subtraction_

String background_subtraction_

protected

◆ compute_peak_quality_

bool compute_peak_quality_

protected

◆ min_peak_width_

double min_peak_width_

protected

◆ min_qual_

double min_qual_

protected

◆ recalculate_peaks_

bool recalculate_peaks_

protected

◆ recalculate_peaks_max_z_

double recalculate_peaks_max_z_

protected

◆ resample_boundary_

double resample_boundary_

protected

◆ stop_after_feature_

int stop_after_feature_

protected

◆ stop_after_intensity_ratio_

double stop_after_intensity_ratio_

protected

◆ use_precursors_

bool use_precursors_

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MRMTransitionGroupPicker()

◆ ~MRMTransitionGroupPicker()

Member Function Documentation

◆ calculateBgEstimation_()

◆ computeQuality_()

◆ createMRMFeature()

◆ findLargestPeak()

◆ operator=()

◆ pickTransitionGroup()

◆ prepareMasterContainer_()

◆ recalculatePeakBorders_()

◆ remove_overlapping_features()

◆ resampleChromatogram_()

◆ selectChromHelper_()

◆ updateMembers_()

Member Data Documentation

◆ background_subtraction_

◆ compute_peak_quality_

◆ min_peak_width_

◆ min_qual_

◆ recalculate_peaks_

◆ recalculate_peaks_max_z_

◆ resample_boundary_

◆ stop_after_feature_

◆ stop_after_intensity_ratio_

◆ use_precursors_